European Commission president José Manuel Barroso was told member states risked making 'an unqualified error'. Photograph: Patrick Hertzog/AFP/Getty Images

The heads of some of the world's leading research organisations have warned the president of the European commission that cuts to the EU science budget will threaten the economic recovery of the region.

A shortfall in science funding would undermine basic training for young researchers and hit major infrastructure projects that are considered crucial for European science and the financial growth of member states, the scientists say in a letter to José Manuel Barroso.

The senior figures at Europe's eight largest research organisations, including the European Space Agency and Cern, home of the Large Hadron Collider, warn that protecting the science budget is "absolutely vital" for "a return to growth" in the region.

Heads of member states are due to decide on funds for science and innovation covering 2014-20 at this week's summit in Brussels. The EU had earmarked €80bn (£65bn) for what it calls the Horizon 2020 budget, which pays for facilities, postdoctoral training and young researchers who are setting up new labs, but that figure is now under negotiation.

Among the projects that may lose out if funding is slashed is Elixir, which aims to link medical information to the human genome and share the results with researchers. The project could help doctors treat individual patients.

The letter states that "at a time when a return to growth is the most pressing policy priority across Europe, it is absolutely vital that investment in our scientific resources – both human and technical – is sustained."

"Science leads the way out of recession, so cutting science budgets is most certainly not the way forward," said Rolf Heuer, the director general of Cern, who signed the letter. "In times of recession, it is incumbent on the public sector to maintain the basic science base, ensuring that there is science for industry to apply.

"We keep hearing that Europe has a shortage of qualified scientists and engineers running to a deficit of tens of thousands of graduates each year. If that's the case in recession, think what the shortage will be when the economy picks up. Cutting science budgets not only damages science in the short term, it passes the wrong message to the young people who could be the scientists and engineers of the future. It would be an unqualified error."

"When it comes to the economy and growth, science and innovation have to be at the centre of that. Unless we make smart decisions now, we're going to get trampled over in the next decade or two. We passionately believe in science, but hard-headed business underpins this." Harrison said.

He said the loss of scientific expertise and hi-tech industry from the region could turn Europe "into a theme park".

Other scientists who signed the letter include Professor Alvaro Giménez Caňete, director of science and robotic exploration at ESA, and Professor Tim de Zeeuw, director general of the European Southern Observatory.

• This article was amended on 23 November 2012 to clarify that member states decide the science budget of 80bn euros, not European Commission officials.